DOKK / manpages / debian 12 / wham-align / wham.1.en
WHAM(1) User Commands WHAM(1)

wham - Wisconsin's High-Throughput Alignment Method

wham [options]* {<readfile> | -1 <m1file> -2 <m2file>} <basepath> <output> <readfile> comma-separated list of files containing unpaired reads <m1file> comma-separated list of files containing upstream mates <m2file> comma-separated list of files containing downstream mates <basepath> write wham data to files with this dir/basename <output> file to write alignments to

use first <int> bases in each read

specify the max number of errors in a reported alignment.
specify the max number of gaps in a reported alignment.
max sum of mismatch quals across alignment
do not align to forward/reverse-complement ref strand
do not align to mate1/mate2 strand: fw/rev, rev/fw.
minimum insert size for paired-end alignment (default: 0).
maximum insert size for paired-end alignment (default: 250).

report up to <int> valid alignemtns per read (default: 1).
report all valid alignments per read.
reprot valid alignments in a sorted order of quality.
discard reads with more than <int> valid alignmetns.

write alignment in SAM format
write aligned reads/pairs to file(s) <fname>
write unaligned reads/pairs to file(s) <fname>

specify the number of threads
do not concatenate results from various threads
specify the number of indexes that fit into memory.

print version information
print this usage message


This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.

February 2021 wham 0.1.5